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N4-Benzoyl-5'-O-DMT-2'-O-MOE-cytidine 3'-CE phosphoramidite
N4-Benzoyl-5'-O-DMT-2'-O-MOE-cytidine 3'-CE phosphoramidite is a modified phosphoramidite designed for efficient and controlled synthesis of RNA and DNA oligonucleotides. The protective groups and modifications, such as N4-benzoyl, 5'-O-DMTr, and 2'-O-MOE, enhance the stability of the resulting nucleic acids and facilitate their incorporation into nucleic acid chains during solid-phase synthesis. This compound is crucial in the production of antisense oligonucleotides, siRNA, probes, and primers, providing enhanced resistance to enzymatic degradation and improved performance in various applications.
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Catalog
BRP-02191
Synonyms
N4-Bz-5'-O-DMTr-2'-O-(2-methoxyethyl)cytidine-3'-CED-phosphoramidite; 2'-O-MOE-C(Bz)-3'-phosphoramidite; N4-Acetyl-5'-O-(4,4'-dimethoxytrityl)-2'-O-methyl-cytidine-3'-CE-cyanoethyl Phosphoramidite; N-Benzoyl-5'-O-[bis(4-methoxyphenyl)(phenyl)methyl]-3'-O-[(2-cyanoethoxy)(diisopropylamino)phosphino]-2'-O-(2-methoxyethyl)cytidine; Cytidine, N-benzoyl-5'-O-[bis(4-methoxyphenyl)phenylmethyl]-2'-O-(2-methoxyethyl)-, 3'-[2-cyanoethyl bis(1-methylethyl)phosphoramidite]; 2'-O-MOE-rC(Bz) Phosphoramidite
CAS
251647-54-8
IUPAC Name
N-[1-[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxy-3-(2-methoxyethoxy)oxolan-2-yl]-2-oxopyrimidin-4-yl]benzamide
Molecular Weight
907.99
Molecular Formula
C49H58N5O10P
Canonical SMILES
CC(C)N(C(C)C)P(OCCC#N)OC1C(OC(C1OCCOC)N2C=CC(=NC2=O)NC(=O)C3=CC=CC=C3)COC(C4=CC=CC=C4)(C5=CC=C(C=C5)OC)C6=CC=C(C=C6)OC
InChI
InChI=1S/C49H58N5O10P/c1-34(2)54(35(3)4)65(62-30-14-28-50)64-44-42(63-47(45(44)60-32-31-57-5)53-29-27-43(52-48(53)56)51-46(55)36-15-10-8-11-16-36)33-61-49(37-17-12-9-13-18-37,38-19-23-40(58-6)24-20-38)39-21-25-41(59-7)26-22-39/h8-13,15-27,29,34-35,42,44-45,47H,14,30-33H2,1-7H3,(H,51,52,55,56)/t42-,44-,45-,47-,65?/m1/s1
InChIKey
IAFVTVZPQIFRAU-NXPFYNPLSA-N
Purity
≥95%
Appearance
White Powder
Storage
Store at -20 °C
Chemical Structure:
Reference Reading
1. A universal, photocleavable DNA base: nitropiperonyl 2'-deoxyriboside
M C Pirrung, X Zhao, S V Harris. J Org Chem. 2001 Mar 23;66(6):2067-71. doi: 10.1021/jo001594r.
A universal, photochemically cleavable DNA base analogue would add desirable versatility to a number of methods in molecular biology. A novel C-nucleoside, nitropiperonyl deoxyriboside (NPdR, P), has been investigated for this purpose. NPdR can be converted to its 5'-DMTr-3'-CE-phosphoramidite and was incorporated into pentacosanucleotides by conventional synthesis techniques. The destabilizing effect on hybrid formation with a complementary strand when this P base opposes A, T, and G was found to be 3-5 kcal/mol, but 9 kcal/mol when it opposes C. Brief irradiation (lambda > 360 nm, 20 min) of DNA containing the P base and piperidine treatment causes strand cleavage giving the 3'- and 5'-phosphates. Two significant recent interests, universal/non-hydrogen-bonding base analogues and photochemical backbone cleavage, have thus been combined in a single molecule that serves as a light-based DNA scissors.
